Obviously i'm biased, but that doesn't mean I don't like the coyote. I would love an 8500rpm screaming NA coyote, it's just not sensible.
But a regular coyote does nothing for me.
When you compare costs (which I have done) you could do a terminator engine for around the same as a coyote.
The problem with that is a coyote without pulling the intake or valve covers is good for mid/low 400's and much lower in torque.
Where's the cobra is a simple pulley and meter away (I bought each for $75 used) from 480rwhp and 500rwtq. Both of which easily out perform the coyote on the low end.
To get a coyote to 03/04 cobra power or above, you either need a power adder (like $5500 worth) or heads, cams and intake which are absurdly expensive.
Even then the terminator is only a
whipple or kenne bell swap away from similar numbers.
My take on it, if low 400's NA are your goals, the coyote is perfect (and you aren't into torque)
If you want somewhere between 450rwhp to 600rwhp, the terminator is the logical choice.
If you need more than that, do whatever you like because it's going to be really expensive no matter how you slice it.
Some other notes, as for head flow? Who really cares when you are just stuffing it full of boost anyway. They aren't like pushrod engines, the really don't need the flow when you add a turbo or SC.
Wiring? For the record, the 03 cobra computer only take a small handful of wires to get to run. I filled an entire bin full of the wiring I pulled out of the harness's. If the condition of the wiring is someone's main worry, they shouldn't be doing a swap at all.